Hi Ritu,
most of the script looks fine. See below for comments.
On 16.02.2012 01:02, Rituparna Sengupta wrote:
> Hi, I tried using 'or'. I didn't get any errors, but now that I'm checking
> the outputs, I found that I got the area for just the ligand and not the
> complex, when I use 'get_area' on the complex. I noticed I get the area for
> whichever (ligand/target) is before the "or" operator, not the one after and
> definitely not for the complex. Here's the code I've been using:
>
> ## r=target(name read as user input)
> ## s=ligand(name read as user input)
>
> e=r+".pdb"
> f=s+".pdb"
> cmd.load(e)
> cmd.load(f)
> cmd.h_add
will do nothing, must be:
cmd.h_add()
> cmd.flag(25, NONE)
did this work for you? NONE should be a string:
cmd.flag(25, "none")
> cmd.set("dot_solvent", 1)
> cmd.set("dot_density", 3)
> ligand_area=cmd.get_area(s)
> target_area=cmd.get_area(r)
> cmd.create("complex", s or r)
This is not a string, but a logical expression on the python level. Must be:
cmd.create("complex", s + " or " + r)
I even prefer:
cmd.create("complex", "(%s) or (%s)" % (s, r))
> complex_area=cmd.get_area("complex")
> contact_area=((ligand_area+target_area)-complex_area)/2
> print ligand_area
> print target_area
> print complex_area
> print contact_area
>
> Thanks in advance.
> Ritu
Cheers,
Thomas
> On 02/13/12, Thomas Holder wrote:
>> Hi Ritu,
>>
>> put "ligand" and "target" in one string as an atom selection with a
>> logical "or".
>>
>> cmd.load("ligand.pdb")
>> cmd.load("target.pdb")
>> cmd.create("complex", "ligand or target")
>>
>> Cheers,
>> Thomas
>>
>> Rituparna Sengupta wrote, On 02/13/12 19:28:
>>> Hi,
>>>
>>> I've just started using PyMol, so this may come across as a stupid
>>> question. I'm using Python to make a plugin for a surface area
>>> calculation. What is the api version for the command:
>>>
>>> create complex, ligand target
>>>
>>> ?(ligand and target are pdb files) I tried using,
>>>
>>> cmd.create(complex, ligand, target)
>>>
>>> but found errors. Apparently I'm supposed to put an integer after the
>>> first two entries in the bracket(according to the 'create' command
>>> api version instructions in the pymol wiki commands section). I tried
>>> loading the molecules separately into 'complex', but the value of the
>>> complex area is different from when loaded together(found this out by
>>> typing directly into pymol). I'll be glad if someone could help.
>>>
>>> Thanks, Ritu
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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